Re: [AMBER] RNA unfolding studies..

From: David A Case <>
Date: Wed, 27 May 2015 08:14:49 -0400

On Wed, May 27, 2015, Asmita Gupta wrote:
> I am studying an RNA hairpin which retains its structure at 25 deg C, but
> melts at physiological temperature (37 deg C).
> available literature on RNA unfolding either deals with force-induced
> unfolding or high temperature MD or REMD.
> Is there any way i can simulate the unfolding pathway/dynamics of this
> structure in far i know, setting up REMD for this small
> temperature scale won't make sense.

Temperature REMD is an excellent way to study equilibrium thermal unfolding
behavior. Once you have established the simulation melting temperature (which
might be quite different thant he experimental one), you can run molecular
dynamics at or near the melting temperature to study the unfolding pathway and
dynamics of the process.

This is a difficult problem to handle with good realism. Be sure you are
familiar with the literature, and be prepared to spend considerable amounts of
your time and computer time. You might want to start with GB simulations to
get experience before moving to explicit solvent simulations. And be aware
that the unfolded ensemble you obtain from simulation may be rather different
from that in the "real" system.


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Received on Wed May 27 2015 - 05:30:02 PDT
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